scPDB - 3k5g entry

Protein Data Bank Entry:

PDB ID : 3k5g

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-10-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-secretase 1
ID:	BACE1_HUMAN
AC:	P56817
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.23.46

Chains:

Chain Name:	Percentage of Residues within binding site
C	100 %

Ligand binding site composition:

B-Factor:	33.940
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.145	985.500

% Hydrophobic	% Polar
35.62	64.38
According to VolSite

Ligand :

HET Code:	BJC
Formula:	C35H52N3O3
Molecular weight:	562.806 g/mol
DrugBank ID:	-
Buried Surface Area:	64.5 %
Polar Surface area:	86.25 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
9.717	-41.7553	48.8329

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C8	CD1	LEU- 30	3.86	0	Hydrophobic	false
C81	CD1	LEU- 30	3.96	0	Hydrophobic	false
O41	OD2	ASP- 32	2.66	160.25	H-Bond (Ligand Donor)	false
O41	OD1	ASP- 32	3.43	142.67	H-Bond (Ligand Donor)	false
N46	O	GLY- 34	2.91	142.87	H-Bond (Ligand Donor)	false
C63	CB	SER- 35	3.85	0	Hydrophobic	false
C67	CB	SER- 35	4.32	0	Hydrophobic	false
C63	CG1	VAL- 69	3.51	0	Hydrophobic	false
C39	CD1	TYR- 71	4.03	0	Hydrophobic	false
C63	CD1	TYR- 71	3.67	0	Hydrophobic	false
C71	CD1	TYR- 71	3.84	0	Hydrophobic	false
C75	CB	TYR- 71	3.9	0	Hydrophobic	false
C27	CG2	THR- 72	4.38	0	Hydrophobic	false
C59	CB	THR- 72	4.22	0	Hydrophobic	false
C24	CB	THR- 72	3.56	0	Hydrophobic	false
C24	CB	GLN- 73	4.31	0	Hydrophobic	false
C85	CB	GLN- 73	4.42	0	Hydrophobic	false
C30	CG	GLN- 73	4.21	0	Hydrophobic	false
O34	N	GLN- 73	3.36	162.84	H-Bond (Protein Donor)	false
C5	CD1	ILE- 110	3.74	0	Hydrophobic	false
C5	CZ2	TRP- 115	4.4	0	Hydrophobic	false
C83	CD1	ILE- 118	3.75	0	Hydrophobic	false
C67	CD1	ILE- 126	3.76	0	Hydrophobic	false
C67	CE1	TYR- 198	4.13	0	Hydrophobic	false
N46	OD2	ASP- 228	2.71	152.61	H-Bond (Ligand Donor)	false
N46	OD2	ASP- 228	2.71	0	Ionic (Ligand Cationic)	false
N35	O	GLY- 230	3	160.53	H-Bond (Ligand Donor)	false
C27	CG2	THR- 231	4.24	0	Hydrophobic	false
C11	CB	THR- 232	4.44	0	Hydrophobic	false
O15	N	THR- 232	2.82	142.47	H-Bond (Protein Donor)	false
O15	OG1	THR- 232	2.6	147.35	H-Bond (Protein Donor)	false
C27	CD	ARG- 235	4.43	0	Hydrophobic	false